Bring what you have. A certified copy might work.

Do i still pay the thousand dollar fine

So, you are looking to adjust based on your brother's petition but you accumulated unlawful presence. 245(i) may help.

What are the options to get her to migrate with my parents?

No options. Only if when parents become LPR they can sponsor her and ask for her early admission into the US based on humanitarian parole.

Can they file regular with the copies of certification? Do they still have to tell USCIS to get the duplicate from DOL?

They will have to request a new original.

May I file a second I539 while current status expires

Well, you can do it, but the last action rule prevails. So, if you have a status right now and will have it by the time your husband files for his...

Can someone help interpret this status? Is there a way to contact DoS or a case officer to inquire if something needs to be done

If anything is needed from you, you will get a letter from the USCIS.

What they do in biometrics test? Is eye scanning neccassary? My wife got pinkeye.

As long as she can keep her eye open, it should not be a problem. However, she should ask to reschedule her appointment due to health issues.

Is there a time frame to submit a motion for reconsideration of a refused immigrant visa at US Consulate?

Technically, you have a year to act from the time of your interview.

For returning resident visa, is it better to apply at port of entry or US Consulate in terms of expected process time at each?

It depends on your circumstances. You should consult with an attorney.

My wife came to the USA with a tourist visa and overstayed for like 5 years then she left .Can I apply for green card for her

Your wife will need a waiver to come back. You should consult with an Immigration attorney.